Science Buddies: "Ask an Expert"

Hi Medical-stuff,

Welcome to Science Buddies! Because each Expert usually checks the forums once a week, it typically takes 1-2 days to get a response to a post. Also, you posted in an existing thread, which did not alert Experts that you were a new user with new questions.

Medical-stuff wrote:Why is it taking so long for the Cancer Genome Anatomy Project website to Email me my information?!

I am not sure what you are expecting to see via e-mail. You can perform this project online through a website: http://cgap.nci.nih.gov/

Medical-stuff wrote:How do you do the hypothesis for the cancer genome anatomy project ????

If you scroll up to earlier in this thread, you will see that Donna Hardy answered a similar question about the hypothesis for this project:

donnahardy2 wrote:In this project you will be comparing the expression of genes in normal and cancer tissue, so you are looking for genes with higher expression levels compared to normal tissue.

Here is the information on the science buddies website for writing your hypothesis:

https://www.sciencebuddies.org/science- ... esis.shtml

You can state your hypothesis something like: “if I compare gene expression in normal and cancer tissue, there will be a higher level of expression in cancer tissue.” And you can be more specific if you are looking at specific genes or types of cancer.

I hope this helps. Please post again (in this same thread) if you have more questions.

Heather

Here is the information on the science buddies website for writing your hypothesis:

https://www.sciencebuddies.org/science- ... esis.shtml

You can state your hypothesis something like: “if I compare gene expression in normal and cancer tissue, there will be a higher level of expression in cancer tissue.” And you can be more specific if you are looking at specific genes or types of cancer. [/quote]

Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

Hi Medical-stuff,

Medical-stuff wrote:Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

It really depends on the gene. The problem with cancer cells is that they grow out of control. There could be an overexpression of genes associated with cell division, or there could be an underexpression of genes meant to stop cell division when space is limited. You can start by focusing on a single gene, and see whether that gene is overexpressed or underexpressed in cancer cells compared to normal cells.

Note that you are not causing the expression to happen. You are looking at what has already happened. So when you ask, "Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?" the answer is yes (for overexpressed genes). That higher expression is exactly what you are measuring. Then you can look at what gene is being overexpressed in cancer cells, and see why that might cause cancer.

Heather

heatherL wrote:Hi Medical-stuff,

Medical-stuff wrote:Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

It really depends on the gene. The problem with cancer cells is that they grow out of control. There could be an overexpression of genes associated with cell division, or there could be an underexpression of genes meant to stop cell division when space is limited. You can start by focusing on a single gene, and see whether that gene is overexpressed or underexpressed in cancer cells compared to normal cells.

Note that you are not causing the expression to happen. You are looking at what has already happened. So when you ask, "Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?" the answer is yes (for overexpressed genes). That higher expression is exactly what you are measuring. Then you can look at what gene is being overexpressed in cancer cells, and see why that might cause cancer.

Heather

So do you think that I should predict which two cancers I think will have similar genes that are over expressed for my hypothesis?

Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

heatherL wrote:Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

What do you mean "having an over expression in the SAME organ"?!
=_=?!

Medical-stuff wrote:

heatherL wrote:Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

What do you mean "having an over expression in the SAME organ"?!
=_=?!

Please help me?!!!!!!!!!!i am doing hypothesis and materials and Procwdure TODAY so I really need a reply before 9:00pm!!!
PLEASE!!!

Heather is given you some great advice and suggestions, and only she can really explain what she meant by that, but I think that she meant that instead of comparing overexpression of genes in different cancers, you might want to consider comparing whether or not the same genes are overexpressed in cancer in the same organ. I think the part that you are misunderstanding is that there is no one type of cancer in an organ. Lung cancer is a general term used to describe many different forms of cancer. Cancer at its simplest is an uncontrolled overgrowth of one type of cell, and since the lung is made up of many different types of cells, there can be many different forms of cancer. Cells are different because each type has a unique purpose, and they all work together to form a functioning organ. Each different type of cell, if it becomes cancerous, causes a different type of cancer (because the cells that cause them are different). Take for example, bronchioalviolar cell carcinoma and squamous cell carcinoma. Both of them occur in the lungs, but bronchioalviolar cell carcinoma occurs in the bronchial cells, while squamous cell carcinoma occurs in squamous cells. So, what I think that Heather was trying to suggest is that you compare the different genes that are overexpressed in two different cancers (bronchioalviolar cell carcinoma and squamous cell carcinoma) that occur in the same organ (lung).

I just want to add that Heather, and all of the other experts, can't always respond before your deadlines because this is not our job, and no one asked us to do this. We all volunteer our time to help you, and all we ask for is a little patience in return. I hope you understand.

Thanks, and I hope I helped!

Meg

Megara7 wrote:Heather is given you some great advice and suggestions, and only she can really explain what she meant by that, but I think that she meant that instead of comparing overexpression of genes in different cancers, you might want to consider comparing whether or not the same genes are overexpressed in cancer in the same organ. I think the part that you are misunderstanding is that there is no one type of cancer in an organ. Lung cancer is a general term used to describe many different forms of cancer. Cancer at its simplest is an uncontrolled overgrowth of one type of cell, and since the lung is made up of many different types of cells, there can be many different forms of cancer. Cells are different because each type has a unique purpose, and they all work together to form a functioning organ. Each different type of cell, if it becomes cancerous, causes a different type of cancer (because the cells that cause them are different). Take for example, bronchioalviolar cell carcinoma and squamous cell carcinoma. Both of them occur in the lungs, but bronchioalviolar cell carcinoma occurs in the bronchial cells, while squamous cell carcinoma occurs in squamous cells. So, what I think that Heather was trying to suggest is that you compare the different genes that are overexpressed in two different cancers (bronchioalviolar cell carcinoma and squamous cell carcinoma) that occur in the same organ (lung).

I just want to add that Heather, and all of the other experts, can't always respond before your deadlines because this is not our job, and no one asked us to do this. We all volunteer our time to help you, and all we ask for is a little patience in return. I hope you understand.

Thanks, and I hope I helped!

Meg

Thank you thank you thank you thank you!!!!you cleared up all my questions&had a very descriptive answer!!!!!but I have just one more question:how can I use the cancer genome anatomy project website for THAT cell?
Science buddies only gives me the way of how to use the website for pancreas cancer.....

Thanks, Meg, for stepping in while I was away.

Medical-stuff wrote:I have just one more question:how can I use the cancer genome anatomy project website for THAT cell?
Science buddies only gives me the way of how to use the website for pancreas cancer.....

The Science Buddies website gives you an example using the pancreas, but the Cancer Genome Anatomy Project website (http://cgap.nci.nih.gov/) allows you to compare the expression of genes for the same cancer in different organs, or to compare different types of cancer in the same organ.

Have you tried playing around on the website yet? I think that it will help for you to check out how the website works and try different things. In fact, playing around with different cancers, different organs, or different genes, might lead you to come up with a new hypothesis! Usually scientists base their hypotheses on their own observations, and then do an experiment to see whether their hypothesis is supported by the data. I suggest that you try out the website and see what you can do with it. Then we can help you hone your particular hypothesis and interpret the data you collect.

Cheers,
Heather

Yes I have done that but I think I'm
Going to do what science buddies procedure is and improvise from that because I don't have a lot if time to finish I have about 1 or 2 weeks
Thank you so so so so so so much!!!!I'll come back with more questions later like graphing and result things...yah stuff like that.Bye:);)I'll be back!!!

No problem. Glad you have a direction. Looking forward to your updates as the project progresses.

Heather

I am still waiting for the cancer genome anayomy project website to send me my email!
It's taking FOREVER!:D
It usually comes at 9:12pm but I may come and ask questions at like 9:30-10
(Just to let you know!):);)

Ok so does it have to be red in the normal part to be cancerous or does it have to be ok the cancer
Side and be red?-the cancer genome anatomy project

Hi
Ok so for my hypothesis for the cancer genome anatomy project I have just learned that pancreas and stomach cancer have the most common over expressed genes

Now what I really need help is on creating a hypothesis for THAT!!!

Hi Medical-stuff,

Medical-stuff wrote:Ok so does it have to be red in the normal part to be cancerous or does it have to be ok the cancer
Side and be red?

The red indicates an overexpression of the gene. There is a column for "Normal" and a column for "Cancer," which tells you whether there is cancer present. Blue indicates a normal expression of the gene, and red indicates an overexpression. The colors do not indicate whether there is cancer present; they are only about gene expression.

Medical-stuff wrote:Ok so for my hypothesis for the cancer genome anatomy project I have just learned that pancreas and stomach cancer have the most common over expressed genes

Now what I really need help is on creating a hypothesis for THAT!!!

I'm not clear on whether you are comparing different cancers or different genes here. Are you saying that many of the same genes are overexpressed in both pancreatic and stomach cancers? Compared to what? Other cancers? Other genes?

You could say something like, "I predict that pancreatic and stomach cancers will have more overlap in gene overexpression compared to lung cancer." Is that what you're trying to see?

Heather

heatherL wrote:Hi Medical-stuff,

Medical-stuff wrote:Ok so does it have to be red in the normal part to be cancerous or does it have to be ok the cancer
Side and be red?

The red indicates an overexpression of the gene. There is a column for "Normal" and a column for "Cancer," which tells you whether there is cancer present. Blue indicates a normal expression of the gene, and red indicates an overexpression. The colors do not indicate whether there is cancer present; they are only about gene expression.

Medical-stuff wrote:Ok so for my hypothesis for the cancer genome anatomy project I have just learned that pancreas and stomach cancer have the most common over expressed genes

Now what I really need help is on creating a hypothesis for THAT!!!

I'm not clear on whether you are comparing different cancers or different genes here. Are you saying that many of the same genes are overexpressed in both pancreatic and stomach cancers? Compared to what? Other cancers? Other genes?

You could say something like, "I predict that pancreatic and stomach cancers will have more overlap in gene overexpression compared to lung cancer." Is that what you're trying to see?

Heather

Ok
So first when u click on a gene then click the person picture,just like science buddies says,and then it shows to sides with it saying cancer and the other side normal if it is red I normal then is it over expressed in cancer or what?

Also
I'm saying that pancreas and stomach cancer both have common genes that are over expressed in cancer
Now I need help writing a hypothesis with THAT.

Here is a guess at how my hypothesis CAN be:
I predict that since pancreas and stomach are close to each other in the body then they will have the same genes that are over expressed.
Correct?
Close?or wrong?
For:the cancer genome anatomy project

Hi Medical-stuff,

Medical-stuff wrote:So first when u click on a gene then click the person picture,just like science buddies says,and then it shows to sides with it saying cancer and the other side normal if it is red I normal then is it over expressed in cancer or what?

Red means the gene is overexpressed. If it is red in the "Normal" column, that means the gene is overexpressed in that organ under normal conditions, or rather that the gene is under-expressed with cancer.

Medical-stuff wrote:I predict that since pancreas and stomach are close to each other in the body then they will have the same genes that are over expressed.
Correct?
Close?or wrong?

I can't tell you whether your hypothesis is right or wrong. Your data will tell you whether your hypothesis is supported! However, I can say that you should base your hypothesis on background research. I'm not sure that the close proximity of the two organs will necessarily mean that the genetic basis of their cancers will be related. If two organs serve similar functions, though, it means that they probably express a lot of similar genes. So it might make sense for two organs with similar functions to have similar gene (over)expression with cancer. Does that make sense?

Heather

WOW!JUST WOW!you have just cleared up a world of mystery and wonder for me!!!!:D
You ARE THE BEST!!!I BET YOUR LIKE A SUPER SMART professor!
Thanks a lot heather!!!!mark my words though,I WILL BE BACK WITH EVEN MORE CONFUSION AS I GO.
Speaking of confusion,how would I do my data?i'm going to start a little more research after I do my health HOmework on endocrine system.

How you do your data will really depend on the question you're asking. If you decide to compare the stomach and pancreas, then you could record the number of overexpressed genes associated with cancer for each organ, noting when the same genes are overexpressed in both organs. You could see whether more genes are overexpressed with cancer compared to normal conditions, and whether the overexpressed genes are usually the same or different for the two organs. Once you have the data, we can talk about the best graphical way to present it...

Heather

Ok so I'm still stuck ok hypothesis apparently no websites talk about organs having same over expressed genes!!:p
Please help me with my hypothesis!

Hi Medical-stuff,

Let's take a step back here. You need to decide what question you want to ask, and it does not have to be a complicated one. What first got you interested in this particular project? Are you trying to learn more about a particular kind of cancer, or are you curious about cancer in general?

I think it may be best for you to focus on one type of cancer (e.g., pancreatic OR stomach cancer), and to figure out which genes are overexpressed. Then you can find out more about those particular genes and their usual function in the cell. Your hypothesis could predict what kind of genes might be overexpressed in cancer cells. For example, you could hypothesize that genes associated with cell division would be overexpressed in cancer cells. There is definitely research out there regarding what genes are generally associated with certain cancers.

I really cannot write your hypothesis for you. You are the one who needs to come up with the research question that interests you. That's why I'm saying you should take a step back for a moment. Think about what made you curious about this project, and ask a question along those lines. What do you hope to learn by doing this project?

Heather

Well I just did some more research and I found out that liver and pancreas both are sending digestive substances to the duodenum...
So I could say...
I hypothesize that the since the pancreas and the liver both are vitual for digesting substances to the duodenum then they will have similar overexpressed genes.

What about that one?

That sounds reasonable. And remember that it's perfectly okay if your hypothesis is not supported by the data. Sometimes you end up with even more interesting results than what you expected to find!

Good luck!

Also how long should my hypothesis be?
What should I write about in my research paper?
How would I make my data graphs/tables?

I hypothesize that since the pancreas and the liver have similar jobs of sending digestive substances to the duodenum them they will also have similar genes that are overexpressed.
Is this a better hypothesis or should I stick To my other one?

Your new hypothesis is well stated. Just remember to include cancer in your hypothesis: "I hypothesize that since the pancreas and the liver have similar jobs of sending digestive substances to the duodenum they will also have similar genes that are overexpressed when cancer develops."

The length of your hypothesis is not important, as long as it clearly states your predictions.

Here is the Science Buddies information about how to write your research paper:
https://www.sciencebuddies.org/science- ... aper.shtml
https://www.sciencebuddies.org/science- ... _Paper.pdf

Here is a sample research paper:
https://www.sciencebuddies.org/science- ... _paper.pdf

Here are tips for data analysis and presentation (graphs and tables):
https://www.sciencebuddies.org/science- ... ysis.shtml
https://www.sciencebuddies.org/science- ... alysis.pdf

Heather

Hi heather !!!
Ok well questions:
For my data would I make graphs showing a gene and how much it is overexpressed in cancer compared to it being under expressed in a normal body?
Also for hypothesis I don't really know what my controlled variable,independent and dependent variables would be.
Also for my research really what you are telling me is that I need to explain my project like tell about pancreas ,functions,pancreas cancer & lung,functions,lung cancer
And should my research paper have like after I finish my actual RESEARCH behind it ,for example,a paper telling materials used,then procedure,etc.?

Ummmm for my hypothesis do I explain what my hypothesis is trying to say and shy I chose it?